library(biovizBase)
library(ggbio)
library(FDb.InfiniumMethylation.hg19)
Known genes:
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
library(EnsDb.Hsapiens.v75)
ensdb <- EnsDb.Hsapiens.v75
library(SNPlocs.Hsapiens.dbSNP144.GRCh37)
snpdb <- SNPlocs.Hsapiens.dbSNP144.GRCh37
options(copdgene_ver_acs = 2)
traits_cont <- copdgene_traits_main()[-1]
traits_bin <- copdgene_traits_main()[1]
traits_all <- c(traits_bin, traits_cont)
Single-trait asosciationr results:
tab1 <- copdgene_results_admixed(traits_cont, "SmokCigNow",
"~/git/hemostat/copdgene/results/07-scan-ver-4/rdata/")
tab2 <- copdgene_results_admixed(traits_cont, "SmokCigNow0_15",
"~/git/hemostat/copdgene/results/07-scan-ver-4/rdata/")
Multi-trait asosciationr results:
massoc1 <- readRDS(file.path(
"~/git/hemostat/copdgene/results/07-scan-ver-4",
"rdata/massoc.interaction.SmokCigNow.rds"))
massoc2 <- readRDS(file.path(
"~/git/hemostat/copdgene/results/07-scan-ver-4",
"rdata/massoc.interaction.SmokCigNow0_15.rds"))
Data description
Results
| Analysis | Tests | Significant | Proprotion | BF Threshold |
|---|---|---|---|---|
| Smoking effects | 484,125 | 525 | 0.108% | 1e-7 |
| Interaction effects | 126,369,511 | 827 | 0.0065% | 3.96e-10 |
| Interaction effects | 195,068,554,297 | 448,242 | 0.00023% | 2.60e-13 |
SmokCigNow)chr <- 11
start <- 12e6
end <- 13e6
gr1 <- GRanges("chr11", IRanges(start, end)) %>% range(ignore.strand = TRUE)
Table of top 10 SNPs:
| rank | snp | zscore | pval | chr | pos | acs | num_snps | size | trait |
|---|---|---|---|---|---|---|---|---|---|
| 1 | rs933920 | 2.928 | 0.003413 | 11 | 12,481,110 | chr11acs76906 | 21 | 36,273 | FEV1pp_utah |
| 2 | rs4553350 | -2.847 | 0.004407 | 11 | 12,759,834 | chr11acs76938 | 29 | 164,946 | FEV1pp_utah |
| 3 | rs11022386 | 2.788 | 0.005301 | 11 | 12,548,017 | chr11acs76922 | 2 | 2,166 | FEV1pp_utah |
| 4 | rs6485989 | 2.719 | 0.006554 | 11 | 12,695,171 | chr11acs76938 | 29 | 164,946 | FEV1pp_utah |
| 5 | rs1564947 | 2.633 | 0.008467 | 11 | 12,176,409 | chr11acs76843 | 24 | 23,173 | FEV1pp_utah |
| 6 | rs4756884 | -2.557 | 0.01055 | 11 | 12,474,098 | chr11acs76906 | 21 | 36,273 | FEV1pp_utah |
| 7 | rs901291 | -2.528 | 0.01146 | 11 | 12,205,793 | chr11acs76851 | 4 | 3,812 | FEV1pp_utah |
| 8 | rs7131034 | -2.499 | 0.01247 | 11 | 12,183,036 | chr11acs76844 | 3 | 576 | FEV1pp_utah |
| 9 | rs10831908 | -2.452 | 0.0142 | 11 | 12,812,419 | chr11acs76938 | 29 | 164,946 | FEV1pp_utah |
| 10 | rs3812760 | 2.447 | 0.0144 | 11 | 12,557,016 | chr11acs76925 | 21 | 25,500 | FEV1pp_utah |
Table of top 10 SNPs of top ancesty segment (chr11acs76906):
| rank | snp | zscore | pval | chr | pos | acs | num_snps | size | trait |
|---|---|---|---|---|---|---|---|---|---|
| 1 | rs933920 | 2.928 | 0.003413 | 11 | 12,481,110 | chr11acs76906 | 21 | 36,273 | FEV1pp_utah |
| 6 | rs4756884 | -2.557 | 0.01055 | 11 | 12,474,098 | chr11acs76906 | 21 | 36,273 | FEV1pp_utah |
| 11 | rs4756866 | -2.369 | 0.01781 | 11 | 12,448,846 | chr11acs76906 | 21 | 36,273 | FEV1pp_utah |
| 23 | rs10831815 | 2.076 | 0.03792 | 11 | 12,446,924 | chr11acs76906 | 21 | 36,273 | FEV1pp_utah |
| 24 | rs10741590 | 2.056 | 0.03976 | 11 | 12,463,318 | chr11acs76906 | 21 | 36,273 | FEV1pp_utah |
| 31 | rs1344615 | -1.901 | 0.05725 | 11 | 12,454,046 | chr11acs76906 | 21 | 36,273 | FEV1pp_utah |
| 53 | rs11022358 | 1.647 | 0.09951 | 11 | 12,470,449 | chr11acs76906 | 21 | 36,273 | FEV1pp_utah |
| 59 | rs10831827 | -1.603 | 0.1089 | 11 | 12,483,197 | chr11acs76906 | 21 | 36,273 | FEV1pp_utah |
| 63 | rs1365403 | 1.571 | 0.1161 | 11 | 12,476,231 | chr11acs76906 | 21 | 36,273 | FEV1pp_utah |
| 67 | rs1346220 | 1.543 | 0.1229 | 11 | 12,480,087 | chr11acs76906 | 21 | 36,273 | FEV1pp_utah |
Gene model tracks:
List of genes: DKK3, MICAL2, MICALCL, PARVA, TEAD1.
Methylation tracks:
| CpG | SNP | Beta | p-value | Methylation Gene |
|---|---|---|---|---|
| cg20233228 | rs16911103 | -4.258 | 4.41e-13 | TEAD1 |
| cg20233228 | rs16911106 | -4.165 | 1.58e-12 | TEAD1 |
Positions of meth. probes:
| CpG | probeStart | probeEnd |
|---|---|---|
| cg20233228 | 12903562 | 12903611 |
Positions of SNPs in COPDGene dataset:
| CpG | SNP | chr | pos |
|---|---|---|---|
| cg20233228 | rs16911103 | NA | NA |
| cg20233228 | rs16911106 | NA | NA |
Positions of SNPs in SNPdb:
| CpG | SNP | chr | pos |
|---|---|---|---|
| cg20233228 | rs16911103 | 11 | 12,343,740 |
| cg20233228 | rs16911106 | 11 | 12,344,805 |
10 (out of 167) rows with the largest effect sizes:
| CpG | SNP | Beta | p-value |
|---|---|---|---|
| cg25413748 | rs658709 | -516.9 | NA |
| cg13569714 | rs10840730 | -278.1 | NA |
| cg20233228 | rs2175132 | -12.58 | NA |
| cg20233228 | rs17036909 | -12.56 | NA |
| cg20233228 | rs1396797 | -12.49 | NA |
| cg20233228 | rs1396795 | -12.49 | NA |
| cg20233228 | rs7953537 | -12.21 | NA |
| cg20233228 | rs17094401 | -12.21 | NA |
| cg20233228 | rs17094405 | -12.2 | NA |
| cg20233228 | rs17094560 | -12.16 | NA |
Positions of meth. probes:
| CpG | probeStart | probeEnd |
|---|---|---|
| cg13569714 | 12,033,074 | 12,033,123 |
| cg25413748 | 12,437,801 | 12,437,850 |
| cg08647724 | 12,479,811 | 12,479,860 |
| cg23384960 | 12,626,522 | 12,626,571 |
| cg20233228 | 12,903,562 | 12,903,611 |
Positions of SNPs (top 10 effect sizes) in SNPdb:
| CpG | SNP | chr | pos |
|---|---|---|---|
| cg25413748 | rs658709 | 20 | 3,587,400 |
| cg13569714 | rs10840730 | 12 | 17,662,085 |
| cg20233228 | rs2175132 | 2 | 69,887,369 |
| cg20233228 | rs17036909 | 2 | 69,883,592 |
| cg20233228 | rs1396797 | 2 | 69,872,657 |
| cg20233228 | rs1396795 | 2 | 69,872,562 |
| cg20233228 | rs7953537 | 12 | 44,693,288 |
| cg20233228 | rs17094401 | 12 | 44,696,784 |
| cg20233228 | rs17094405 | 12 | 44,700,415 |
| cg20233228 | rs17094560 | 12 | 44,769,768 |
--- orthogonalizing from global acs.
Reading /Users/andreyziyatdinov/git/hemostat/copdgene/procdata/finemap/gdat2_chr11.rds
Reading /Users/andreyziyatdinov/git/hemostat/copdgene/procdata/finemap/gdat2_chr11.bed
SmokCigNow0_15)chr <- 2
start <- 237.75e6
end <- 239e6
end2 <- 240e6
gr2 <- GRanges("chr2", IRanges(start, end)) %>% range(ignore.strand = TRUE)
Table of top 10 SNPs:
| rank | snp | zscore | pval | chr | pos | acs | num_snps | size | trait |
|---|---|---|---|---|---|---|---|---|---|
| 1 | rs7597880 | -2.801 | 0.005097 | 2 | 2.38e+08 | chr2acs210672 | 2 | 84 | FVC_utah |
| 2 | rs12613388 | -2.759 | 0.005791 | 2 | 238,660,169 | chr2acs210750 | 3 | 3,957 | FVC_utah |
| 3 | rs3739051 | -2.616 | 0.008892 | 2 | 2.39e+08 | chr2acs210780 | 1 | 0 | FVC_utah |
| 4 | rs2280289 | 2.369 | 0.01786 | 2 | 238,483,729 | chr2acs210712 | 21 | 56,543 | FVC_utah |
| 5 | rs7597414 | -2.264 | 0.02359 | 2 | 2.38e+08 | chr2acs210671 | 1 | 0 | FVC_utah |
| 6 | rs2701336 | 2.261 | 0.02375 | 2 | 237,906,903 | chr2acs210664 | 1 | 0 | FVC_utah |
| 7 | rs2279642 | -2.228 | 0.02591 | 2 | 238,682,770 | chr2acs210753 | 21 | 97,602 | FVC_utah |
| 8 | rs6431563 | 2.223 | 0.02621 | 2 | 238,804,355 | chr2acs210764 | 1 | 0 | FVC_utah |
| 9 | rs2701337 | -2.218 | 0.02659 | 2 | 237,909,007 | chr2acs210665 | 1 | 0 | FVC_utah |
| 10 | rs10187629 | -2.211 | 0.02701 | 2 | 238,640,263 | chr2acs210747 | 2 | 1,258 | FVC_utah |
Table of top 10 SNPs of top ancesty segment (chr2acs210712):
| rank | snp | zscore | pval | chr | pos | acs | num_snps | size | trait |
|---|---|---|---|---|---|---|---|---|---|
| 4 | rs2280289 | 2.369 | 0.01786 | 2 | 238,483,729 | chr2acs210712 | 21 | 56,543 | FVC_utah |
| 31 | rs7598559 | 1.683 | 0.09237 | 2 | 238,435,398 | chr2acs210712 | 21 | 56,543 | FVC_utah |
| 42 | rs13394555 | 1.548 | 0.1217 | 2 | 238,483,322 | chr2acs210712 | 21 | 56,543 | FVC_utah |
| 56 | rs10190103 | 1.338 | 0.181 | 2 | 238,482,636 | chr2acs210712 | 21 | 56,543 | FVC_utah |
| 114 | rs2325814 | -0.9431 | 0.3456 | 2 | 238,462,725 | chr2acs210712 | 21 | 56,543 | FVC_utah |
| 124 | rs6705903 | -0.9155 | 0.3599 | 2 | 238,433,955 | chr2acs210712 | 21 | 56,543 | FVC_utah |
| 125 | rs2292881 | 0.9096 | 0.363 | 2 | 238,434,249 | chr2acs210712 | 21 | 56,543 | FVC_utah |
| 151 | rs2292877 | -0.7854 | 0.4322 | 2 | 238,458,180 | chr2acs210712 | 21 | 56,543 | FVC_utah |
| 154 | rs1979763 | -0.781 | 0.4348 | 2 | 238,436,481 | chr2acs210712 | 21 | 56,543 | FVC_utah |
| 159 | rs6766 | 0.7544 | 0.4506 | 2 | 238,483,164 | chr2acs210712 | 21 | 56,543 | FVC_utah |
Gene model tracks:
List of genes: COL6A3, COPS8, LRRFIP1, MLPH, PRLH, RAB17, RAMP1, RBM44, SCLY, UBE2F, UBE2F-SCLY.
Methylation tracks:
List of (sorted) genes: ASB1, COL6A3, COPS8, ESPNL, HDAC4, HES6, ILKAP, KLHL30, LINC01107, LINC01940, LOC151174, LRRFIP1, MIR4440, MLPH, PER2, PRLH, RAB17, RAMP1, RBM44, SCLY, TRAF3IP1, TWIST2, UBE2F, UBE2F-SCLY.